Rebecca Sun & Thomas Girke

Sunday, December 9, 2012 1:30–6 p.m.

Category: TrainingDescription: Description: This workshop will cover the most common SNP/Var-Seq data analysis routines. It will include the following topics: (1) read mapping with variant aware aligners; (2) SNP/indel calling; (3) handling of standard variant data formats such as VCF; (4) annotating variants with genomic context information including variant mapping to genes, intergenic regions; (5) identification of synonymous/non-synonymous SNPs; (6) injecting identified variants into reference genome/proteome; and (7) variant viewing using R graphics and the IGV genome browser. Basic knowledge of the R software including sequence handling routines, as introduced in the "Introduction to R" and Basic NGS tutorials, will be expected in this workshop. Manual for this workshopMaximum number of participants: 40

Registration fee*: no charge for participants from registered labs, $23 for UCR members, $75 for participants from external academic institutions, and $102 for participants from commercial institutions.

Laptop requirements: Participants will work during the course on a Linux cluster. Personal laptops are required to log remotely into the cluster. For this, all laptops need to have a functional wireless connection. In addition, they will need a terminal application and a SCP software for file exchange. Windows users should install for this purpose PuTTY and WinSCP. On Mac OS X systems, one can use the native terminal application and Fugu for file exchange. Linux systems usually have similar applications pre-configured.Open to: General PublicAdmission: Entry Charge: Sponsor: Institute for Integrative Genome Biology